Last year I flew to Johannesburg on LH A380 business from Frankfurt and returned on SAA to UK (forget if it was the A330 or A340). Personally I found the new business on LH more comfortable in lay flat, food a bit better and service a bit better. I know some people do prefer SAA but if repeating I'd select LH both directions. If you have a choice, try doing 1 each direction (both are *A) - wasn't a huge difference between each and for me I'm glad I experienced both.
note: neither are PODs like Air Canada (mentioning because I see you're from Canada as well). On that trip I'd rank LH (service and cool factor of A380 with full level of business class)>AC>SAA.
note: if the cost was the same I'd do SAA from NY to JNB for convenience (one red-eye vs. 2, avoid an 8 hour layover in Europe).
Enjoy the trip!